MolNFT v1 · #52372 · protein

Crystal structure of the T. thermophilus dodecin W38F mutant

2VYX · TTHA1431: “Crystal structure of the T. thermophilus dodecin W38F mutant”. X-ray diffraction, 4 ligands (FMN, COA, NA), 15 pockets (best druggability 0.71). MolNFT v1 #52372 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2VYX
Type: protein
Length: 804 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TTHA1431
UniProt: Q5SIE3
Ligands: FMN, COA, NA, CL
Pockets: 15 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, F, G, H, I, J	TTHA1431	protein	67	22% helix, 58% strand	Q5SIE3
B, L	TTHA1431	protein	66	23% helix, 59% strand	Q5SIE3
C, K	TTHA1431	protein	68	22% helix, 57% strand	Q5SIE3

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 12 copies · chains A, B, H, G, C, F, E, J, L, D, K, I
COA · Coenzyme A · ligand · 12 copies · chains A, H, L, B, F, G, C, E, J, D, I, K
NA · Sodium ion · metal · chains D, I
CL · Chloride ion · ion · 4 copies · chains A, H, L, B, F, G, C, E, J, D, I, K

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	735	0.71	0.77	96	CL
2	342	0.64	0.79	31	FMN
3	334	0.64	0.79	29	FMN
4	321	0.64	0.80	30	FMN
5	421	0.63	0.77	61	CL, COA

Interfaces

30 interfaces between chains.

A–B · 627 Å² buried · 10 hydrogen bonds · protein-protein
J–L · 623 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 623 Å² buried · 10 hydrogen bonds · protein-protein
J–K · 622 Å² buried · 10 hydrogen bonds · protein-protein
G–I · 621 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2VYX · Crystal structure of the T. thermophilus dodecin W38F mutant · the same entry in another collection · chain L against L, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q5SIE3
Elsewhere: RCSB PDB 2VYX · PDBe 2VYX · UniProt Q5SIE3

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